{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Lluis Hernandez"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16259"],"description":["To characterize the transcriptional impact of MALAT1 in MCL a RNAseq was performed on three SOX11-positive PDLS-MCL samples comparing MALAT1-silenced PDLS to paired controls, all cultured with pro-proliferative factors."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Cells were grown with IL4, CD40L, HA-tag and BAFF as described in Araujo et al 2023 (PMID: 37031299)","Nucleic Acid Extraction - Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen), quantified with Qubit, and quality-checked using Tapestation 4200 (Agilent).","Sample Treatment - Silencing was performed using MALAT1 specific LNA-Gapmer (Qiagen) at 1micromolar vs Scrambled LNA-Gapmer (Qiagen) by gymnotic delivery along 5 days.","Sample Collection - Peripheral blood was extracted and PBMC purified with Ficoll and cryopreserved in liquid nitrogen until the day of the experiment.","Library Construction - Libraries were prepared from 10 ng of total RNA using the TAKARA_SMART-Seq® Total RNA Pico Input (ZapR® Mammalian) kit (following the manufacturer’s instructions).","Sequencing - Libraries were sequenced using a NextSeq2000 (Illumina, Inc.) in paired-end mode with a read length of 2×50 bp, generating more than 60 million paired-end reads per sample."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - For the analysis of RNAseq data, ribosomic RNA reads were filtered out using SortMeRNA (version 4.3.4).","Sequence Alignment - Kallisto (version 0.46.1). was used for   high throughput sequence alignment protocol"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Lluis Hernandez"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq of MALAT1 silencing experiments in three Patient derived lymphoma spheroids (PDLS) from Mantle Cell Lymphoma (MCL) patients","description":"To characterize the transcriptional impact of MALAT1 in MCL a RNAseq was performed on three SOX11-positive PDLS-MCL samples comparing MALAT1-silenced PDLS to paired controls, all cultured with pro-proliferative factors.","dates":{"release":"2026-01-07T00:00:00Z","modification":"2026-01-07T02:02:39.152Z","creation":"2025-11-22T20:43:43.467Z"},"accession":"E-MTAB-16259","cross_references":{"ENA":["ERP185506"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}